ELN for Academic Research: A Success Story

September 11, 2023

The Problems with Paper Notebooks

“Hey, I think someone ran that reaction a few years ago, why don’t you go check in their notebook?”

Have you heard this request from your PI and immediately thought…

Yeah. I’ve been there.

I remember thinking even if I managed to find the right page, I would have to undertake a second and equally arduous journey to find the associated NMR spectra and other characterization data.

Safe to say that in the digital age… Data is King

The ability to digitally store, share, mine, and process data is the foundation of how we work today. So why as chemists and biologists in academia are we continuing to confine our most valuable data, our experimental records, to paper notebooks on neglected shelves, the same way scientists have done since the 19th century?

In the age of database searches, word processing, file sharing, and email surely there must be a way to digitize the scientific process?

These were the questions being asked in Prof. Shih-Yuan Liu’s Research Group at Boston College in 2015 when we decided to start the search for an electronic lab notebook (ELN).

The ELN Solution: Digital Notebook, Searchable Database

Aside from a searchable data repository for all our reactions, there were other features motivating us to make the jump from paper to digital. We were looking for a way to standardize lab notebook entries to improve record keeping and a platform that would encourage collaboration and information sharing.

Most organic chemists are familiar with the software ChemDraw®, the chemical sketcher tool; we knew that having a similar sketcher in a digital notebook entry would save a lot of time over hand-drawing reaction schemes. Organic chemists often run the same or similar reactions multiple times, therefore having the ability to copy or refer to experiments would be very useful.

In a paper notebook, the lack of a copy-paste feature fosters some poor record-keeping habits, such as certain lab member’s tendency to just write “see page XX” instead of filling in crucial reaction details for a repeated reaction.

While the benefits of features like copy-paste seemed pretty straight-forward, we did not have a sense of the life-changing improvements adopting an ELN would bring prior to starting our evaluations. 

Here are the three important lessons I learned about finding ELN that is right for my lab:

1) Use the ELN as if it were already your notebook!
While it takes more effort, the only way to put an ELN through its paces is to record real experiments with real data. A few days of using an ELN provided a good picture of how it would fare over the next few years.

2) No ELN is perfect!
Just like with any software, there will be some quirks and features that not all users will like. Decide as a group what aspects of the software are simply inconvenient and which ones are deal breakers.

3) Change is difficult!
Adopting a new piece of software or learning how to use any new tool can be a challenging process. Be patient, stick with it, and form a consensus on how the new software will be implemented.

Following our review process, the Scilligence ELN became our ELN of choice with its combination of an excellent search feature, convenience, time saving tools such as copy experiments, reagent lookup, direct integration with NMR, robust performance, and competitive price point.

The Scilligence team worked closely with us to deploy their web-based software, trained us on how to use it, and applied a few customizations.

A few months after we started our search for an ELN, we bid farewell to paper notebooks!

Experiencing the benefits of adopting the Scilligence ELN right off the bat!

Several features of the Single Step Reaction form, an ideal template for synthetic organic chemistry experiments, significantly reduced data entry time. The reaction scheme editor populates reagents from a database search, simultaneously pulling in key information like MW and MF. The stoichiometry table automatically calculates amounts and ratios. After the software does most of the heavy lifting by filling in the reaction scheme data, generating a procedure is even more straightforward.

With the recipe feature, a scientist can generate a generalized experiment template and share it with the whole group; the recipe pulls in reagent information, leaving only a few minor adjustments to be made.

In addition to saving time for individual notebook entries, the ELN makes information sharing much more efficient. Our group used the project documents as a central location for sharing references, SOP’s, presentations and other group project materials. Before the ELN, we had to recreate all our paper reaction schemes in ChemDraw® and then paste them into PowerPoint slides for group meetings. Using the ELN allowed us to start holding group meetings and presentations right in the ELN environment, with researchers projecting their notebook pages on a presentation screen.

Professor Liu could now monitor the entire groups’ notebooks from the comfort of his own desk!

I experienced the greatest impact of using the Scilligence ELN when it came time to write my thesis.

Instead of having to dig through instrument computers to track down data, process that raw analytical data into spectra, and chase down that one reaction with the highest yield, all my data was already present in a centralized, fully searchable database.

I defended my PhD thesis at Boston College in May 2019 and went on to work in materials research at a government contractor. This year I returned to Scilligence as an employee, working as an Application Scientist in Presales Support. The Boston College Chemistry Department continues to use Scilligence ELN and to build an ever-expanding database that will be far more valuable to researchers than forgotten notebooks on dusty shelves!

Scilligence is working on an ELN catered to academic institutions so that more student researchers can access the tremendous benefits of a digital scientific workflow. This ELN will streamline the lab notebook experience and encourage collaboration by providing a digitized and paperless way to work on experiments and projects at every step. Browse experiments across multiple notebooks, harmonize the format of data content, quickly search for specific information, and prevent the loss of existing laboratory knowledge when researchers leave.